rs481809

Variant names:

• chr3-101293262-C-G
• rs481809
• NM_016247.4:c.502-1752G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016247.4(IMPG2):​c.502-1752G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,072 control chromosomes in the GnomAD database, including 40,380 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40380 hom., cov: 31)
• Consequence: IMPG2 NM_016247.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

Genes affected

IMPG2 (HGNC:18362): (interphotoreceptor matrix proteoglycan 2) The protein encoded by this gene binds chondroitin sulfate and hyaluronan and is a proteoglycan. The encoded protein plays a role in the organization of the interphotoreceptor matrix and may promote the growth and maintenance of the light-sensitive photoreceptor outer segment. Defects in this gene are a cause of retinitis pigmentosa type 56 and maculopathy, IMPG2-related.[provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IMPG2	NM_016247.4	c.502-1752G>C		intron_variant	Intron 3 of 18	ENST00000193391.8	NP_057331.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IMPG2	ENST00000193391.8	c.502-1752G>C		intron_variant	Intron 3 of 18	1	NM_016247.4	ENSP00000193391.6

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109152 AN: 151954 Hom.: 40349 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.706

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.718 AC: 109215 AN: 152072 Hom.: 40380 Cov.: 31 AF XY: 0.724 AC XY: 53850 AN XY: 74334

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.708

Alfa AF: 0.748 Hom.: 5437

Bravo AF: 0.705

Asia WGS AF: 0.774 AC: 2692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.83
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs481809; hg19: chr3-101012106;